diff --git a/ms2/test/src/org/labkey/test/ms2/QuantitationTest.java b/ms2/test/src/org/labkey/test/ms2/QuantitationTest.java
index 0f8ff8157..3aad4168c 100644
--- a/ms2/test/src/org/labkey/test/ms2/QuantitationTest.java
+++ b/ms2/test/src/org/labkey/test/ms2/QuantitationTest.java
@@ -20,11 +20,14 @@
 import org.labkey.test.BaseWebDriverTest;
 import org.labkey.test.Locator;
 import org.labkey.test.categories.Daily;
+import org.labkey.test.categories.MS2;
+import org.labkey.test.categories.XTandem;
 import org.labkey.test.components.ui.lineage.LineageGraph;
+import org.labkey.test.util.PipelineAnalysisHelper;
 
 import java.io.File;
 
-@Category({Daily.class})
+@Category({Daily.class, MS2.class, XTandem.class})
 @BaseWebDriverTest.ClassTimeout(minutes = 4)
 public class QuantitationTest extends AbstractXTandemTest
 {
@@ -34,6 +37,8 @@ public class QuantitationTest extends AbstractXTandemTest
         "<?xml version=\"1.0\" encoding=\"UTF-8\" ?> \n" +
         "<bioml>\n" +
             "  <note label=\"pipeline, protocol name\" type=\"input\">" + LIBRA_PROTOCOL_NAME + "</note> \n" +
+            "  <note label=\"pipeline, database\" type=\"input\">Bovine_mini1.fasta</note>\n" +
+            "  <note label=\"protein, cleavage site\" type=\"input\">[KR]|{P}</note>\n" +
             "  <note label=\"pipeline, protocol description\" type=\"input\">Search with Libra quantitation</note> \n" +
             "  <note label=\"pipeline prophet, min peptide probability\" type=\"input\">0</note> \n" +
             "  <note label=\"pipeline prophet, min protein probability\" type=\"input\">0</note> \n" +
@@ -55,20 +60,15 @@ public void testSteps()
 
         setupEngine();
 
-        waitForElement(Locator.xpath("//select[@name='sequenceDB']/option[.='" + DATABASE1 + "']" ), WAIT_FOR_JAVASCRIPT);
         log("Set analysis parameters.");
-        setFormElement(Locator.name("protocolName"), LIBRA_PROTOCOL_NAME);
-        setFormElement(Locator.name("protocolDescription"), "Search with Libra quantitation");
-        selectOptionByText(Locator.name("sequenceDB"), DATABASE1);
-        setFormElement(Locator.name("configureXml"), "");
-        waitAndClick(Locator.xpath("//a[@class='labkey-button']/span[text() = 'OK']"));
-        setFormElement(Locator.name("configureXml"), LIBRA_INPUT_XML);
-        clickButton("Search");
+        PipelineAnalysisHelper helper = new PipelineAnalysisHelper(this);
+        helper.waitForProtocolSelect();
+        helper.setProtocol(LIBRA_PROTOCOL_NAME, LIBRA_INPUT_XML);
+        helper.setDescription("Search with Libra quantitation");
+        clickButton("Analyze");
+
         log("View the analysis log.");
-        // Search is submitted as AJAX, and upon success the browser is redirected to a new page. Wait for it to load
-        waitForElement(Locator.linkWithText("Data Pipeline"), WAIT_FOR_JAVASCRIPT);
-        sleep(5000); // without this sleep, some machines try to redirect back to the begin.view page after the Data Pipeline link is clicked
-        clickAndWait(Locator.linkWithText("Data Pipeline"));
+        goToModule("Pipeline");
 
         String runDescription = SAMPLE_BASE_NAME + " (" + LIBRA_PROTOCOL_NAME + ")";
         waitForPipelineJobsToComplete(1, runDescription, false);
diff --git a/ms2/test/src/org/labkey/test/tests/ms2/XTandemTest.java b/ms2/test/src/org/labkey/test/tests/ms2/XTandemTest.java
index b760e3b6d..533f342ff 100644
--- a/ms2/test/src/org/labkey/test/tests/ms2/XTandemTest.java
+++ b/ms2/test/src/org/labkey/test/tests/ms2/XTandemTest.java
@@ -32,6 +32,7 @@
 
 import java.io.File;
 
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -48,7 +49,6 @@ public class XTandemTest extends AbstractXTandemTest
     protected static final String SEARCH_FIND_FASTA3 = "search target ribosomal protein S16 (BS17)";
     protected static final String PROTOCOL = "X!Tandem analysis";
     protected static final String PEPTIDE_CROSSTAB_RADIO_PROBABILITY_ID = "peptideProphetRadioButton";
-    protected static final String PEPTIDE_CROSSTAB_RADIO_PROBABILITY_VALUE = "probability";
     protected static final String PEPTIDE_CROSSTAB__PROBABILITY_TEXTBOX_NAME = "peptideProphetProbability";
     protected static final String PEPTIDE_CROSSTAB_RADIO_NAME = "peptideFilterType";
     protected static final String PEPTIDE_CROSSTAB_RADIO_VALUE_NONE = "none";
@@ -59,7 +59,7 @@ public void testSteps()
         log("Verifying that pipeline files were cleaned up properly");
         File test2 = new File(PIPELINE_PATH + "/bov_sample/" + SEARCH_TYPE + "/test2");
         if (test2.exists())
-            fail("Pipeline files were not cleaned up; test2("+test2.toString()+") directory still exists");
+            fail("Pipeline files were not cleaned up; test2("+ test2 +") directory still exists");
 
         basicMS2Check();
     }
@@ -157,7 +157,7 @@ private void verifyComparePeptides()
         setFormElement(Locator.name("minimumProbability"), "");
         clickButton("Search");
         clickAndWait(Locator.id("expandCollapse-ProteinSearchProteinMatches"), 0);
-        assertTrue(!(isTextPresent(SEARCH_FIND_FASTA1) || isTextPresent(SEARCH_FIND_ALT_FASTA1)));
+        assertFalse(isTextPresent(SEARCH_FIND_FASTA1) || isTextPresent(SEARCH_FIND_ALT_FASTA1));
         assertTextNotPresent(SEARCH_FIND_FASTA1);
         assertTextPresent("No data to show");